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The USS Enterprise-D is on a charting mission in the Morgana Quadrant. CommanderRiker is taking part in one of Worf's calisthenicsholodeck programs. They are both attacked by a different monster but eventually both monsters are defeated. After defeating his monster Worf, energized by Klingon bloodlust, nearly attacks Riker until Riker orders him "at ease!" When the program ends, Riker asks Worf if all his workout programs are like this. However, Worf admits that others are more intense but "too personal" to share.

On the bridge, Data detects an unusual reading from his station, an area of total blackness, seemingly devoid of space, matter and energy. It is like a "hole in space." CaptainPicard orders a probe to be launched into it. However, as soon as it enters the void it disappears. This alarms Worf and he recommends raising shields, for the void reminds him of a Klingon legend about a space creature that devours "entire vessels". He soon realizes that he is being foolish, and Picard orders another probe to be launched. This second probe also vanishes, more quickly than the last.

A hole in space

EnsignCrusher tells Picard that he can determine the boundaries of the anomaly based on where the two probes disappears and suggests that he can bring the ship closer. Picard agrees and orders Crusher to bring the ship in closer using thrusters only. Suddenly, the blackness expands and envelopes the Enterprise.

Data tries to scan the surrounding area, but there is absolutely nothing to see. Picard decides to proceed with the mission and orders Crusher to set a course out of the void, back the way they came. However, no matter how fast or how far they go, they cannot leave. They drop a beacon in order to help them get a fix on their position. They set off on a course away from the beacon, yet soon enough they are approaching it again. They are going in circles. Picard orders full stop.

"Our sister ship!"

Suddenly, they detect a decloaking RomulanD'deridex-classWarbird approaching them. Riker heads to join Worf at tactical while bringing the ship to red alert; ordering the photon torpedoes armed. Picard orders them to hold for his order as he sits down. When Wesley spots the ship decloaking, the Warbird fires on them as the Enterprise takes a direct hit with significant weakening of their shields. Picard issues a warning to the attacking ship that they'll return fire. When the message is transmitting, Worf informs the captain the warbird has armed another full spread. The Enterprise returns fire with a single torpedo, destroying their attacker immediately. Picard laments that the battle was too easy and Data can detect no debris from the Romulan ship. Another ship appears on sensors. This time it is the Galaxy-classUSS Yamato, their sister ship. They hail the vessel but there is no response. Sensors also detect no life signs. Riker recommends sending an away team over. Picard agrees, but only to have a minimal away team go over. Riker chooses Worf and they leave the bridge for the transporter room.

Armed with phasers and equipped with tricorders, Riker orders Miles O'Brien to beam them over to the bridge. On board, they find out they are not on the bridge, instead in corridors and furthermore, hear screams with no one to be found. They find that the ship makes no structural sense. When they do reach the bridge, there appear to be several of them. When one walks through a door, they wind up not where they expected. This situation infuriates Worf and he begins to lose his temper. However, Riker calms him down.

Meanwhile, relief conn officer Ensign Haskell on the Enterprise detects a gap, through which stars can be seen. It appears to be a way to escape, but Picard will not leave without the away team. The starfix suddenly disappears.

Suddenly, the Yamato too begins to vanish. Picard orders O'Brien to beam the away team back immediately. O'Brien succeeds, in the nick of time. Riker comes to the bridge, very agitated. He has had enough and suggests that they "put all this technology to work, and get the hell out of here!"

Another starfix soon appears. A pleased Picard orders Ensign Haskell to set a course towards it, but as soon as this is done, it quickly closes again. Another starfix appears, but once again vanishes when a course is set towards it. Yet another starfix appears, but Picard ignores it, having enough of it. Haskell observes that it seems closer than the others, yet Picard still holds position. Dr.Pulaski thinks that the crew is being treated like "rats in a maze". CounselorTroi says that she can sense a vast intelligence at work. Picard has had enough of responding to stimuli and decides to do nothing from now on.

Suddenly, a disjointed face appears on the screen. It introduces itself as Nagilum. It inquires about Pulaski's "construction" and how it differs from most of the other people on the bridge. Pulaski explains that she and Troi are female and that the others are male. Picard says that these differences are necessary for the propagation of the species. Nagilum asks for a demonstration of this but Pulaski refuses this request.

"You exist, and then you cease to exist."

Nagilum then inquires about Humans' "limited existence", in which "you exist, then you cease to exist. Your minds call it… death." Suddenly, Haskell begins to shake violently. He grabs his face in a vain effort to control himself, but falls from his station screaming. He collapses on the floor, in a fetal-position, with his hands clasped over his mouth and dies with his eyes still open. Pulaski rushes to help him, but there is nothing that can be done. Nagilum watches his victim die, fascinated. "How interesting", he mutters. Pulaski confirms with her tricorder that Haskell is dead, and an angry Picard declares, "We cannot allow you to do that! We will fight you!"

Nagilum replies that in order to completely understand death, he is going to have kill about a third of the ship's crew, possibly up to a half; he then absentmindedly muses on how he will need to observe "every kind of dying" as Picard and the rest of the bridge are rendered speechless, visibly blanching at the thought of such unspeakable suffering being inflicted so wantonly on the crewmembers of the Enterprise…

Picard calls a staff meeting in the observation lounge and opts to initiate the ship's auto-destruct sequence rather than allow the entity to perform any more experiments on them and slaughter more of the crew. In engineering, Picard and Riker set the sequence for twenty minutes, an interval Riker thinks is a nice, round number for the Enterprise's complement to prepare for their deaths.

Picard, while preparing himself in his quarters for the destruction of the ship, as well as his death, is visited by Data and Troi to discuss death and the implications of death. After a short discussion, Picard realizes that both are merely Nagilum in disguise, and that they are trying to trick him into aborting the self-destruct. Picard verifies Data's location, which is on the bridge. "It's not going to work, Nagilum," he says. The two impostors vanish and suddenly the ship is back in normal space.

Picard goes to the bridge to make sure that they are free. With only a few seconds left to spare, he orders the computer to stop the countdown. When asked if he concurs, Riker replies, "Yes! Absolutely! I do indeed concur! Wholeheartedly!" The sequence stops and Picard jokingly informs Riker that a simple "yes" would have sufficed. Riker remarks that he didn't want there to be any chance of a misunderstanding by the ship's computer.

"As species, we have no common ground."

Picard goes to his ready room and hopes that Nagilum got what he wanted. Suddenly, Nagilum appears on Picard's desktop monitor, and informs Picard that he got much more than he needed. Nagilum reports his conclusions to Picard. He says that Humans "seem to find no tranquility in anything. You struggle against the inevitable. You thrive on conflict. You are rash, quick to judge, slow to change. It's amazing you've survived. As a species, we have no common ground. You are too aggressive. Too hostile. Too militant". Picard does not argue with him, but points out that they do indeed have one trait in common, curiosity. Nagilum, with a Human-like chuckle, agrees. Picard also says that they may meet again, but that next time, it will be out among the stars. Nagilum fades off screen.

Picard then returns to the bridge, and orders Crusher to put them back on their original course. Riker tells him to steer clear of "any holes".

"I think it is perhaps best to be ignorant of certain elements of Klingon psyche."

- Picard

"Like the rat said: you can keep the cheese--I just want to get out of the trap."

- La Forge

"Captain, the most elementary and valuable statement in science, the beginning of wisdom, is 'I do not know.'"

- Data to Picard

"Remember the course in ancient history at Starfleet Academy? About the time when men still believed the Earth was flat?""Mm, and that the sun revolved around it.""And that if a ship sailed too far out into the ocean it would fall off the edge of the world?""Mm. Beyond this place, there be dragons."

- Riker and Picard

"I have a question, sir."
"Yes Data, what is it?"
"What is death?"
"Oh, is that all? Oh, Data, you're asking probably the most difficult of all questions. Some see it as a changing into an indestructible form, forever unchanging; they believe that the purpose of the entire universe is to maintain that form in an earth-like garden which will give delight and pleasure through all eternity. On the other hand, there are those who hold to the idea of our blinking into nothingness. That all of our experiences and hopes and dreams, merely a delusion."
"Which do you believe, sir?"
"Considering the marvelous complexity of the universe, its clockwork perfection, its balances of this against that, matter, energy, gravitation, time, dimension, I believe that our existence must be more than either of these philosophies. That what we are goes beyond Euclidean or other "practical" measuring systems, and that our existence is part of a reality beyond what we understand now as reality."

- Nagilum as Data and the real Picard

"…Ten seconds to auto-destruct…"
"Captain…"
"Abort auto-destruct sequence."
"Riker, William T., do you concur?"
"Yes! Absolutely! I do indeed concur whole-heartedly!"
"Auto-destruct canceled."
"A simple 'yes' would have sufficed, Number One."
"I didn't want there to be any chance of a misunderstanding."

- the Computer, Picard, and Riker

"A ship has one bridge! ONE BRIDGE!! ONE RIKER!! ONE BRIDGE!!!"

- An angry Worf, on the duplicated bridge of the USS Yamato

"Why do I get the feeling that this was not the time to join this ship?"

- Dr. Pulaski after the decision has been reached to self-destruct the ship.'

"Sensors show nothing out there, absolutely nothing."
"Sure is a damned ugly nothin'."

- Data and La Forge

"Speaks right up for something your sensors say isn't there, Data."

- La Forge, after Nagilum yells at the bridge crew

"I understand. The masculine and the feminine."
"It is the way in which we propagate our species."
"Please, demonstrate how this is accomplished."
"Not likely."

For Kolbe, the challenge was to make the show visually interesting while shooting five days on the bridge set. He noted, "The bridge is intriguing when you step on it for the first time and you look at it for about ten minutes. Then it becomes an utter crashing bore, because it's nothing but tan walls and a few twinkling lights. I did a lot of choreography on that show. It's probably the script that has the most notes on where actors move – every step, which I very rarely do. I usually like the actors to drive themselves where they have to go. On something like 'Where Silence Has Lease' you have to keep the camera constantly moving, and that was a hell of a challenge. I spent a lot of time on that bridge on my belly, hanging down from the rafters and in any other position to try and figure out what I would do with the camera." (Captains' Logs: The Unauthorized Complete Trek Voyages, p. 173)

As he awaits the Enterprise self-destruct countdown in his quarters, Picard listens to Trois Gymnopédies (specifically, Gymnopedie No 1. Lent et Douloureux, translated: Slow and Painful), by Erik Satie, a French composer and pianist.

As Worf and Riker are exploring the derelict USS Yamato, in the moment when Riker notes the chemical composition of the bulkheads, the first door on the right-hand side of the blind corridor outside the transporter room can be seen open. This is one of only two instances in the entire seven-year run of the series that this door is seen open, with the other in "11001001" as Picard requests access to the Weapons Room. In Star Trek: The Motion Picture, that door had served as the entrance to the transporter room of the original USS Enterprise, while the wider door used in TNG had not been added yet. When the sets were redesigned for their appearances in The Next Generation, the back wall of the transporter room was moved closer to the transporter platform, and the space behind it was left open for possible use later. It should be noted that for both of these instances there was no standing set behind that door. The room behind the door was used as the sickbayscience laboratory set in such episodes as "Home Soil" and "Evolution".

The false Yamato bridge has a notable sound effect: a subtly distorted version of the Enterprise bridge background noises, indicating that things are not quite right aboard the Yamato.

Near the end of the previous episode, "The Child", before leaving Science Station Tango Sierra, we see Picard mentioning Morgana Quadrant as the new destination. Indeed, according to the Captain's log, the present episode takes place in the Morgana Quadrant.

Worf's Klingon legend about a space creature eating starships may have some basis in fact, as seen in VOY: "Bliss" where just such a creature is encountered. It also might refer to the giant space amoeba in TOS: "The Immunity Syndrome".

The original USS Enterprise encountered a "hole" in space which couldn't be penetrated by sensors in the "The Immunity Syndrome", yet Data states "There is no record of any Federation vessel encountering anything remotely like this."

The registry of the USS Yamato is NCC-1305-E in this episode, but was changed to NCC-71807 for "Contagion".

While the false Yamato bridge is seen to be an exact copy of the Enterprise bridge in this episode, the bridge of the real Yamato is shown to have very subtle physical differences in "Contagion".

O'Brien, manning the transporter during this episode, is referred to as "lieutenant" by Riker, suggesting that he is a commissioned officer. Later episodes contradict this, and O'Brien would eventually be the token enlisted man on both TNG and Star Trek: Deep Space Nine. See also: Miles O'Brien's rank history

This episode marks the first appearance of the new red alert lights which entirely flash on and off and they will be used for the rest of the show's run.

This is the only episode where Picard says "come in" when his doorbell rings. The rest of the episodes have him saying "come".

In "11001001", when the self-destruct is set, Riker expresses his concern about the computer allotting a five-minute countdown. Picard agrees, but says "there is no other option". In this episode, the countdown now has a option to set the amount of time until the ship self destructs. When Picard hears the computer ask for the time interval, he says "interesting question", suggesting it was a change he'd not known about until that moment. It could be the result of the computer system upgrade the Enterprise was supposed to get in the mentioned episode.

The musical cue heard just after Riker beams aboard the USS Yamato is the same choral synthesizer note used approximately seven minutes into Part II of "The Best of Both Worlds", when Captain Picard is given a robotic arm covering by the Borg. The musical cue that is heard during the activation of the auto-destruct sequence by Picard and Riker and when Picard tests whether Nagilum truly let the Enterprise escape, is reused at the end of the Season 3 episode "Booby Trap", when Picard navigates the Enterprise out of the asteroid field.

The music to all three episodes was scored by veteran composer Ron Jones.

There are hints of the classic Star Trek "Fight Music" (see TOS: "Amok Time") in the holodeck scene with Riker and Worf.

Maurice Hurley was quite pleased with the majority of the show, although he felt that the ending didn't work. He stated, "What that show was to me was our guys at three in the morning, they hear a noise in the attic. I put a pillow over my head and go back to sleep and hope it's nothing. They got up to find out, 'Oh boy, what is it?' That's what the show was." The story appealed to Hurley as it was true to the series' premise of exploration. "I hate to keep saying it, monsters and creatures just didn't work. One of the things that sometimes has to be remembered, and I forgot it as much as anybody, was that you forget these are scientists out here, not soldiers. They're out there to learn, so that sense of learning and investigation is really important, more important than all of the running and jumping, more important than the Ferengi, more important than the Borg, more important than any of that stuff is to deal with an idea or something new." (Captains' Logs: The Unauthorized Complete Trek Voyages, p. 173)

Director Winrich Kolbe thought the premise was interesting, although he wished it could have been further developed. He noted, "We look at things in our little universe and interpret people in a certain way and they make sense of us or they don't make sense of us. A foreigner, for instance. The way he or she thinks or sees things. You put that in outer space and have a totally different organization looking at us, now it seems to me that you want to push it further. You want that experiment to go further and us become almost like whatever they want us to be. Unfortunately it didn't go so far. That is probably my major beef." Kolbe noted this was due to the limits of episodic drama. "[Y]ou only have 44 minutes and in those 44 minutes, unless you do story arcs, if you have to go out there and come back in 44 minutes you're kind of handicapped. You don't want to go out too far so you lose your audience and never catch them as you come back." (Captains' Logs: The Unauthorized Complete Trek Voyages, p. 173)

Winrich Kolbe also remembers, "That was murder. It was five days on the bridge. To shoot that long on the bridge was the worst experience I've ever had. I don't necessarily mean that in negative terms. It was just very challenging. That's where I began to move the camera. In the end, I think it's one of the best ones I've done." (The Official Star Trek: The Next Generation Magazine issue 21, p. 30)